CFAP58 is involved in the sperm head shaping and flagellogenesis of cattle and mice.

CFAP58 is a testis-enriched gene that plays an important role in the sperm flagellogenesis of humans and mice. However, the effect of CFAP58 on bull semen quality and the underlying molecular mechanisms involved in spermatogenesis remain unknown. Here, we identified two single-nucleotide polymorphisms (rs110610797, A>G and rs133760846, G>T) and one indel (g.-1811_ g.-1810 ins147bp) in the promoter of CFAP58 that were significantly associated with semen quality of bulls, including sperm deformity rate and ejaculate volume. Moreover, by generating gene knockout mice, we found for the first time that the loss of Cfap58 not only causes severe defects in the sperm tail, but also affects the manchette structure, resulting in abnormal sperm head shaping. Cfap58 deficiency causes an increase in spermatozoa apoptosis. Further experiments confirmed that CFAP58 interacts with IFT88 and CCDC42. Moreover, it may be a transported cargo protein that plays a role in stabilizing other cargo proteins, such as CCDC42, in the intra-manchette transport/intra-flagellar transport pathway. Collectively, our findings reveal that CFAP58 is required for spermatogenesis and provide genetic markers for evaluating semen quality in cattle.

The Construction of the Self-Induced Sal System and Its Application in Salicylic Acid Production.

The design and construction of more complex and delicate genetic control circuits suffer from poor orthogonality in quorum sensing (QS) systems. The Sal system, which relies on salicylic acid as a signaling molecule, is an artificially engineered regulatory system with a structure that differs significantly from that of natural QS signaling molecules. Salicylic acid is an important drug precursor, mainly used in the production of drugs such as aspirin and anti-HIV drugs. However, there have been no reports on the construction of a self-induced Sal system in single cells. In this study, a high-copy plasmid backbone was used to construct the regulatory proteins and a self-induced promoter of salicylic acid in E. coli by adjusting the precise regulation of key gene expression; the sensitivity and induction range of this system were improved. Subsequently, the exogenous gene pchBA was introduced in E. coli to extend the shikimate pathway and synthesize salicylic acid, resulting in the construction of the first complete self-induced Sal system. Finally, the self-induced Sal System was combined with artificial trans-encoded sRNAs (atsRNAs) to repress the growth-essential gene ppc and accumulate the precursor substance PEP, thereby increasing the titer of salicylic acid by 151%. This construction of a self-induced artificial system introduces a new tool for selecting communication tools and induction systems in synthetic biology and metabolic engineering, but also demonstrates a self-inducible pathway design strategy for salicylic acid biosynthesis.

EGR1-CCL2 Feedback Loop Maintains Epithelial-Mesenchymal Transition of Cisplatin-Resistant Gastric Cancer Cells and Promotes Tumor Angiogenesis.

BACKGROUND: The mechanism of cisplatin resistance in gastric cancer (GC) is still elusive; several recent evidences proposed that chemoresistant tumor cells acquired aggressive behaviors. AIMS: This study was aimed to investigate the mechanism of epithelial-mesenchymal transition (EMT) and angiogenesis in chemoresistant GC. METHODS: Bioinformatics analysis and function or mechanism experiments including RT-qPCR, immunofluorescence, Western blot, luciferase reporter assay, Chromatin immunoprecipitation, Chicken chorioallantoic membrane assay and animal experiments were applied to evaluate the role of EGR1-CCL2 feedback loop. RESULTS: Compared with the parental cell line SGC7901, cisplatin resistant SGC7901R cells underwent EMT and showed increased angiogenic capabilities. Mechanistically, SGC7901R cells showed increased levels of EGR1, which could transcriptionally activate the angiogenic factor CCL2 and EMT regulator ZEB2. Reciprocally, CCL2 activated the CCR2-ERK-ELK1-EGR1 pathway, thus forming a positive feed-forward loop. Moreover, CCL2 in culture medium of SGC7901R cells promoted angiogenesis of Human Umbilical Vein Endothelial Cells (HUVECs). EGR1 expression was positively correlated with CCL2 and ZEB2 in clinical GC tissues, and the depletion of ERG1 could also decrease microvessel density and ZEB2 expression in metastatic nodules of nude mice. CONCLUSIONS: EGR1-CCL2 feedback loop might exert critical roles on EMT and angiogenesis of chemoresistant GC.

Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle.

Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.

Integrated transcriptomics and metabolomics analyses reveal benzo[a]pyrene enhances the toxicity of mercury to the Manila clam, Ruditapes philippinarum.

Mercury (Hg2+) and benzo[a]pyrene (BaP) are ubiquitous and persistent pollutants with multiple toxicities in bivalve molluscs. Here, the toxicological responses in the gills of Manila clams, Ruditapes philippinarum, to Hg2+ (10 µg L-1), BaP (3 µg L-1), and their mixture were analysed using transcriptomics and metabolomics approaches. Comparisons of the transcriptomes and metabolomes of Hg2+-and/or BaP-treated clams with control animals revealed the involvement of the detoxification metabolism, immune defence, energy-related pathways, and osmotic regulation in the stress response of R. philippinarum. Exposure to Hg2+ alone primarily enhanced the detoxification and energy metabolic pathways by significantly increasing the expression of genes associated with heat-shock proteins and oxidative phosphorylation. However, co-exposure to Hg2+ and BaP caused greater immunotoxicity and disrupted detoxification metabolism, the TCA cycle, glycolysis, and ATP generation. The expression levels of cytochrome P450 1A1 (CYP1A1), multidrug resistance-associated protein 1 (MRP1), and myosin (MYO), and the activity of electron transport system (ETS) in gills were detected, supporting the underlying toxic mechanisms of Hg2+ and BaP. We suggest that the presence of BaP enhances the toxicity of Hg2+ by 1) hampering the detoxification of Hg2+, 2) increasing the immunotoxicity of Hg2+, and 3) constraining energy availability for clams.

Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows.

BACKGROUND: Neutrophils are the first effectors of inflammatory response triggered by mastitis infection, and are important defense cells against pathogenic Escherichia coli (E. coli). DNA methylation, as a critical epigenetic mechanism for regulating gene function, is involved in bovine mastitis. RESULTS: In this study, we sequenced the blood neutrophils of healthy and E. coli-infected mastitic half-sib cows for the overall DNA methylation levels using transcriptome sequencing and reduced representation bisulfite sequencing. The methylation levels in the mastitis cows (MCs) were decreased compared with healthy cows (HCs). A total of 494 differentially methylated regions were identified, among which 61 were up-methylated and 433 were down-methylated (MCs vs. HCs). The expression levels of 1094 differentially expressed genes were up-regulated, and 245 genes were down-regulated. Twenty-nine genes were found in methylation and transcription data, among which seven genes' promoter methylation levels were negatively correlated with expression levels, and 11 genes were differentially methylated in the exon regions. The bisulfite sequencing PCR and quantitative real-time PCR validation results demonstrated that the promoter methylation of CITED2 and SLC40A1 genes affected differential expression. The methylation of LGR4 exon 5 regulated its own alternative splicing. The promoter methylation of bta-miR-15a has an indirect effect on the expression of its target gene CD163. The CITED2, SLC40A1, and LGR4 genes can be used as candidates for E. coli-induced mastitis resistance. CONCLUSIONS: This study explored the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-induced mastitis, thereby helping explain the function of DNA methylation in the pathogenesis of mastitis and provided new target genes and epigenetic markers for mastitis resistance breeding in dairy cattle.

Novel human monoclonal antibodies targeting the F subunit of leukocidins reduce disease progression and mortality caused by Staphylococcus aureus.

BACKGROUND: Staphylococcus aureus is a leading cause of Gram-positive bacterial infections worldwide; however, the treatment of S. aureus infection has become increasingly difficult due to the prevalence of methicillin-resistant S. aureus strains, highlighting the urgent need for the development of novel strategies. The complexity of S. aureus pathogenesis relies on virulence factors. Recent studies have demonstrated that leukocidins expressed by the majority of clinical isolates play important roles in the pathogenesis of S. aureus. RESULTS: In this study, we developed three human monoclonal antibodies against all F-components of leukocidins HlgABC, LukSF, and LukED with high affinity. These antibodies were found to be capable of blocking leukocidin-mediated cell lysis in vitro. Furthermore, the antibodies dramatically reduced disease progression and mortality after S. aureus infection in vivo. CONCLUSIONS: Our findings revealed that neutralizing bicomponent leukocidins may be a promising strategy to combat infections caused by S. aureus.

Two Trichome Birefringence-Like Proteins Mediate Xylan Acetylation, Which Is Essential for Leaf Blight Resistance in Rice.

Acetylation is a ubiquitous modification on cell wall polymers, which play a structural role in plant growth and stress defenses. However, the mechanisms for how crop plants accomplish cell wall polymer O-acetylation are largely unknown. Here, we report on the isolation and characterization of two trichome birefringence-like (tbl) mutants in rice (Oryza sativa), which are affected in xylan O-acetylation. ostbl1 and ostbl2 single mutant and the tbl1 tbl2 double mutant displayed a stunted growth phenotype with varied degree of dwarfism. As shown by chemical assays, the wall acetylation level is affected in the mutants and the knock-down and overexpression transgenic plants. Furthermore, NMR spectroscopy analyses showed that all those mutants have varied decreases in xylan monoacetylation. The divergent expression levels of OsTBL1 and OsTBL2 explained the chemotype difference and indicated that OsTBL1 is a functionally dominant gene. OsTBL1 was found to be Golgi-localized. The recombinant OsTBL1 protein incorporates acetyl groups onto xylan. By using xylopentaose, a preferred acceptor substrate, OsTBL1 can transfer up to four acetyl residues onto xylopentaose, and this activity showed saturable kinetics. 2D-NMR spectroscopy showed that OsTBL1 transfers acetate to both 2-O and 3-O sites of xylosyl residues. In addition, ostbl1 and tbl1 tbl2 displayed susceptibility to rice blight disease, indicating that this xylan modification is required for pathogen resistance. This study identifies the major genes responsible for xylan acetylation in rice plants.

Transcriptome analysis of the Yesso scallop, Patinopecten yessoensis gills in response to water temperature fluctuations.

Water temperature fluctuations are considered to be a major factor affecting the immune functions and metabolic processes of scallops. To better understand the immune defense mechanisms of Yesso scallop, Patinopecten yessoensis following exposure to water temperature fluctuations, transcriptomic profiles in the gills from high-frequency fluctuations (HF_G), low-frequency fluctuations (LF_G), and no fluctuations (NF_G) groups were obtained using HiSeq™ 2500 (Illumina). For HF_G, scallops were transferred directly between 18 and 8 °C every 4 h and for 10 fluctuations, while scallops in LF_G were transferred between 18 and 13 °C every 12 h, for a total of 4 fluctuations. A total of 442,922,590 clean reads were generated in 9 libraries and then assembled into 210,780 unigenes with an average length of 705 bp and an N50 of 1253 bp. Based on sequence similarity, 54,529 unigenes (25.87%) were annotated in at least one database. Comparative analysis revealed that 696 unigenes differentially expressed in temperature stressed groups compared with the control, including 229 unigenes between HF_G and NF_G, and 548 unigenes between LF_G and NF_G, respectively. Additionally, among these differentially expressed genes (DEGs), there were 41 immune-related unigenes and 16 protein metabolism-related unigenes. These results provide fundamental information on the molecular defense mechanisms in the Yesso scallop gills after exposure to water temperature fluctuations.

Prevalence and Causes of Visual Impairment in a Chinese Adult Population: The Taizhou Eye Study.

PURPOSE: To study the current prevalence and causes of low vision and blindness in an adult Chinese population. DESIGN: Population-based, cross-sectional study. PARTICIPANTS: We used a random cluster sampling method and evaluated 10 234 eligible subjects ≥45 years old (response rate, 78.1%) in the Taizhou Eye Study. METHODS: Examinations were performed from July 2012 through December 2013. Participants underwent a detailed examination, including uncorrected visual acuity, best-corrected visual acuity (BCVA), intraocular pressure, axial length, slit-lamp, and fundus examinations to evaluate the prevalence and primary causes of visual impairment (VI). MAIN OUTCOME MEASURES: We defined low vision and blindness according to the World Health Organization (WHO) criteria (low vision: BCVA, <20/63-≥20/400; blindness: BCVA, <20/400 in the better eye) and United States criteria (low vision: BCVA, <20/40-≥20/200; blindness: BCVA, <20/200 in the better eye). RESULTS: Using the WHO BCVA criteria, the standardized prevalence of bilateral low vision and blindness were 5.1% and 1.0%, respectively. Using the United States BCVA criteria, the standardized prevalence were 12.8% and 1.5%, respectively. Using the WHO criteria, the primary causes of bilateral low vision and blindness were cataract (59.1% and 48.5%, respectively), myopic macular degeneration (17.6% and 17.2%, respectively), and age-related macular degeneration (11.6% and 10.1%, respectively). The primary causes of monocular low vision were cataract (55.6%), age-related macular degeneration (12.6%), and myopic macular degeneration (8.9%), whereas those of monocular blindness were cataract (46.8%), atrophy of eyeball or prosthetic eye (10.2%), and cornea opacity (7.3%). A further analysis revealed that in adults 45-59 years old, myopic macular degeneration (59.6% and 27.2%, respectively) and cataract (13.8% and 23.4%, respectively) were the leading causes of bilateral and monocular VI. In adults ≥60 years old, cataract (66.8% and 61.2%, respectively) and age-related macular degeneration (12.6% and 11.8%, respectively) were the primary causes of bilateral and monocular VI. CONCLUSIONS: The prevalence of low vision and blindness in Chinese adults remains a severe public health problem. In the Taizhou Eye Study, cataract was the leading cause of low vision and blindness. Myopic macular degeneration and cataract were the primary causes of VI in adults 45-59 years and ≥60 years old, respectively.

Contributions of Visuo-oculomotor Abilities to Interceptive Skills in Sports.

PURPOSE: Monitoring and intercepting a fast approaching object is a critical skill for many sports. Athletes might be distinguished from nonathletes based on their ability to access various visual abilities to accomplish interceptive actions. Here, we examined whether interceptive visuomotor skills of athletes and nonathletes are differently correlated to a hierarchy of visuo-oculomotor abilities related to the perception of motion in depth. METHODS: Eighty-six athletes in interceptive sports, as well as 60 nonathletes, were recruited based on their sport performance and prior experiences. Their basic visual abilities (dominant eye acuity, contrast sensitivity, visual span, and visual memory) and complex visuo-oculomotor abilities (dynamic acuity, accommodative facility, near point of convergence, and near/far phoria) were analyzed in relation to critical visuomotor skills (manual interception, visually guided locomotion, and depth judgment). RESULTS: Discriminant analysis revealed that athletes and nonathletes can be accurately differentiated based on measured visuomotor skills (91.3% accuracy, p < 0.0001). Near point of convergence, accommodative facility, and dynamic acuity were moderately effective in identifying athletes (71.3%, p = 0.002) and in predicting the three visuomotor skills (all r(2) ≥ 0.096, all p ≤ 0.022). Dominant eye acuity and contrast sensitivity also identified athletes (61.4%, p = 0.021) and contributed to complex visuo-oculomotor abilities (all r(2) ≥ 0.046, all p ≤ 0.039). The correlations among measured abilities were more significant for athletes than nonathletes. CONCLUSIONS: Athletes in interceptive sports are superior to nonathletes in their visuomotor skills. They also have broader access to various visual and complex visuo-oculomotor abilities than nonathletes. This likely allows athletes to more effectively coordinate visual and oculomotor abilities under demanding conditions when some visual cues are degraded. The present findings are consistent with a pyramid of sports vision and suggest a top-down process for athlete screening and training.

RNAIII suppresses the expression of LtaS via acting as an antisense RNA in Staphylococcus aureus.

RNAIII is known as the key effector of staphylococcal accessory gene regulator (agr) quorum-sensing system, which plays a central role in the pathogenesis of Staphylococcus aureus. As a regulatory RNA, RNAIII regulates multiple targets, including exoproteins and cell-wall-associated proteins. Lipoteichoic acid synthase (LtaS) is involved in the synthesis of lipoteichoic acid (LTA) that is one of the major components of cell wall. The chemical compound targeting to LtaS decreases S. aureus growth via blocking LTA production. Until now, the regulatory mechanism of LtaS expression is still not clear. The level of ltaS mRNA in S. aureus is analyzed by semi-quantitative RT-PCR analysis and qRT-PCR. The protein level of LtaS is determined by Western blotting. The putative interaction sites between RNAIII and LtaS mRNA are predicted. And LtaS-5ºUTR-lacZ and LtaS-5ºUTR-mutant-lacZ reporter vectors are constructed according to the putative interaction sites. Our data show that the expression of ltaS is regulated by RNAIII in S. aureus. The level of LtaS is significantly higher in the RNAIII deficient strain compared to its parent strain. In the further investigation, 5ºUTR of ltaS was predicted to be the putative interaction site of RNAIII. The results of detection of ß-galactosidase activities suggest that RNAIII can inhibit the expression level of LtaS through acting on the 5ºUTR region of LtaS mRNA. Our finding presents that LtaS is another target of RNAIII and RNAIII suppresses the expression of LtaS via acting as an antisense RNA in S. aureus.

Retention of OsNMD3 in the cytoplasm disturbs protein synthesis efficiency and affects plant development in rice.

The ribosome is the basic machinery for translation, and biogenesis of ribosomes involves many coordinated events. However, knowledge about ribosomal dynamics in higher plants is very limited. This study chose a highly conserved trans-factor, the 60S ribosomal subunit nuclear export adaptor NMD3, to characterize the mechanism of ribosome biogenesis in the monocot plant Oryza sativa (rice). O. sativa NMD3 (OsNMD3) shares all the common motifs and shuttles between the nucleus and cytoplasm via CRM1/XPO1. A dominant negative form of OsNMD3 with a truncated nuclear localization sequence (OsNMD3(ΔNLS)) was retained in the cytoplasm, consequently interfering with the release of OsNMD3 from pre-60S particles and disturbing the assembly of ribosome subunits. Analyses of the transactivation activity and cellulose biosynthesis level revealed low protein synthesis efficiency in the transgenic plants compared with the wild-type plants. Pharmaceutical treatments demonstrated structural alterations in ribosomes in the transgenic plants. Moreover, global expression profiles of the wild-type and transgenic plants were investigated using the Illumina RNA sequencing approach. These expression profiles suggested that overexpression of OsNMD3(ΔNLS) affected ribosome biogenesis and certain basic pathways, leading to pleiotropic abnormalities in plant growth. Taken together, these results strongly suggest that OsNMD3 is important for ribosome assembly and the maintenance of normal protein synthesis efficiency.

MicroRNA-30a promotes B cell hyperactivity in patients with systemic lupus erythematosus by direct interaction with Lyn.

OBJECTIVE: To investigate why the level of Lyn is significantly decreased in B cells from a majority of patients with systemic lupus erythematosus (SLE) and to determine the role of microRNA-30a (miR-30a) in SLE B cell hyperactivity. METHODS: Luciferase reporter gene assays were performed to identify the interaction between miR-30a and the 3'-untranslated region (3'-UTR) of Lyn. Levels of miR-30a in B cells were determined by TaqMan quantitative polymerase chain reaction (qPCR), Lyn messenger RNA levels were tested with real-time qPCR, and protein levels of Lyn were determined using Western blotting. The quantity of IgG was determined by enzyme-linked immunosorbent assay. The proliferation of B cells was measured using (3) H-thymidine incorporation. RESULTS: In B cell lines, miR-30a, but not miR-30b, miR-30c, miR-30d, or miR-30e, could specifically bind the 3'-UTR of Lyn, and overexpression of miR-30a inhibited the levels of Lyn. The level of miR-30a in B cells was significantly higher in SLE patients compared to healthy donors. The level of miR-30a was negatively associated with the level of Lyn in B cells. Overexpression of miR-30a was found to promote B cell proliferation and the production of IgG antibodies. The effect of miR-30a could be abrogated by inducing overexpression of Lyn in B cells. CONCLUSION: These results reveal that elevated expression of miR-30a is responsible for the reduction in levels of Lyn in B cells from patients with SLE, suggesting that miR-30a plays an important role in B cell hyperactivity.

Notopterygium incisum Root Extract (NRE) Alleviates Epileptiform Symptoms in PTZ-Induced Acute Seizure Mice.

BACKGROUND: Epilepsy is a common neurological disorder affecting more than 70 million people worldwide. Despite numerous efforts on new antiepileptic drugs, approximately one-third of epilepsy patients suffer from uncontrolled seizures. It leads to serious psychosocial consequences, cognitive problems, and decreased quality of life. OBJECTIVE: Our previous studies have shown that N. incisum root extract (NRE) can improve cognitive dysfunction in Alzheimer's disease (AD) mice. In addition, our research shows that AD and epilepsy have pathological mechanisms overlapping. Therefore, we tried to investigate whether NRE can ameliorate the seizures of epileptic mice in this study. METHODS: NRE-treated mice group was given an oral administration with 1 g/kg/d for 7 days. On the 8th day, mice were exposed to PTZ (i.p. injection) to induce epilepsy. Then the cognitive tests of mice in the water maze were carried out, and the biochemical indexes and pathological tests were carried out after the mice were sacrificed. RESULTS: SOD level in the NRE group was significantly higher than that in the PTZ group, while MDA, TNF-α, and IL-1ß levels were decreased. The cognitive ability of NRE-treated mice was significantly improved compared with the PTZ group. Immunohistochemistry (IHC) results showed that the activation of microglia and astrocytes in the hippocampus and cortex of NRE mice were inhibited. CONCLUSION: This study suggests that NRE can alleviate epilepsy and improve cognitive function in mice with epilepsy, and its mechanism may be through reducing inflammation and enhancing antioxidant defense.

Atomically Dispersed Fe-N4 Sites and NiFe-LDH Sub-Nanoclusters as an Excellent Air Cathode for Rechargeable Zinc-Air Batteries.

The sluggish four-electron processes of the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) limit the development of rechargeable Zn-air batteries (RZABs). Highly efficient ORR/OER bifunctional electrocatalysts are therefore highly desired for the commercialization of RZABs in large scale. Herein, the Fe-N4-C (ORR active sites) and NiFe-LDH clusters (OER active sites) are successfully integrated within a NiFe-LDH/Fe,N-CB electrocatalyst. The NiFe-LDH/Fe,N-CB electrocatalyst is first prepared by the introduction of Fe-N4 into carbon black (CB), followed by the growth of NiFe-LDH clusters. The cluster nature of NiFe-LDH effectively avoids the blocking of Fe-N4-C ORR active centers and affords excellent OER activity. The NiFe-LDH/Fe,N-CB electrocatalyst thus exhibits an excellent bifunctional ORR and OER performance, with a potential gap of only 0.71 V. The NiFe-LDH/Fe,N-CB-based RZAB exhibits an open-circuit voltage of 1.565 V and a specific capacity of 731 mAh gZn-1, which is much better than the RZAB composed of Pt/C and IrO2. Particularly, the NiFe-LDH/Fe,N-CB-based RZAB displays excellent long-term charging/discharging cyclic stability and rechargeability. Even at a large charging/discharging current density (20 mA cm-2), the charging/discharging voltage gap is only ∼1.33 V and exhibits an increase smaller than 5% after 140 cycles. This work provides a new low-cost bifunctional ORR/OER electrocatalyst with high activity and superior long-term stability and will be helpful to the commercialization of RZAB in large scale.

Unraveling the salt tolerance of Phi29 DNA polymerase using compartmentalized self-replication and microfluidics platform.

In Phi29-α-hemolysin (α-HL) nanopore sequencing systems, a strong electrochemical signal is dependent on a high concentration of salt. However, high salt concentrations adversely affect polymerase activity. Sequencing by synthesis (SBS) requires the use of phi29 polymerase without exonuclease activity to prevent the degradation of modified nucleotide tags; however, the lack of exonuclease activity also affects polymerase processivity. This study aimed to optimize phi29 polymerase for improved salt tolerance and processivity while maintaining its lack of exonuclease activity to meet the requirements of nanopore sequencing. Using salt tolerance compartmentalized self-replication (stCSR) and a microfluidic platform, we obtained 11 mutant sites with enhanced salt tolerance attributes. Sequencing and biochemical analyses revealed that the substitution of conserved amino acids such as G197D, Y369E, T372N, and I378R plays a critical role in maintaining the processivity of exonuclease-deficient phi29 polymerase under high salt conditions. Furthermore, Y369E and T372N have been identified as important determinants of DNA polymerase binding affinity. This study provides insights into optimizing polymerase processability under high-salt conditions for real-time polymerase nanopore sequencing, paving the way for improved performance and applications in nanopore sequencing technologies.

Identifying mitophagy-related genes as prognostic biomarkers and therapeutic targets of gastric carcinoma by integrated analysis of single-cell and bulk-RNA sequencing data.

Gastric carcinoma (GC) is the fourth leading cause of cancer-related mortality worldwide. Patients with advanced GC tend to have poor prognoses and shortened survival. Finding novel predictive biomarkers for GC prognosis is an urgent need. Mitophagy is the selection degradation of damaged mitochondria to maintain cellular homeostasis, which has been shown to play both pro- and anti-tumor effects. This study combined single-cell sequencing data and transcriptomics to screen mitophagy-related genes (MRGs) associated with GC progression and analyze their clinical values. Reverse transcription-quantitative PCR (RT-qPCR) and immunochemistry (IHC) further verified gene expression profiles. A total of 18 DE-MRGs were identified after taking an intersection of single-cell sequencing data and MRGs. Cells with a higher MRG score were mainly distributed in the epithelial cell cluster. Cell-to-cell communications among epithelial cells with other cell types were significantly upregulated. We established and validated a reliable nomogram model based on DE-MRGs (GABARAPL2 and CDC37) and traditional clinicopathological parameters. GABARAPL2 and CDC37 displayed different immune infiltration states. Given the significant correlation between hub genes and immune checkpoints, targeting MRGs in GC may supplement more benefits to patients who received immunotherapy. In conclusion, GABARAPL2 and CDC37 may be prognostic biomarkers and candidate therapeutic targets of GC.

Signatures of selection in indigenous Chinese cattle genomes reveal adaptive genes and genetic variations to cold climate.

Cold climate shapes the genome of animals and drives them to carry sufficient genetic variations to adapt to changes in temperature. However, limited information is available about the genome-wide pattern of adaptations to cold environments in cattle. In the present study, we used 777K SNP genotyping (15 Chinese cattle breeds, 198 individuals) and whole genome resequencing data (54 cattle breeds of the world, 432 individuals) to disentangle divergent selection signatures, especially between the cold-adapted (annual average temperature of habitat, 6.24 °C to 10.3 °C) and heat-adapted (20.2 °C to 24.73 °C) Chinese native cattle breeds. Genomic analyses revealed a set of candidate genes (e.g., UQCR11, DNAJC18, EGR1, and STING1) were functionally associated with thermogenesis and energy metabolism. We also characterized the adaptive loci of cattle exposed to cold temperatures. Our study finds new candidate genes and provides new insights into adaptations to cold climates in cattle.

Cold climates can affect cattle performance, survival, and health. Local cattle breeds have been adapted to the local environments including extremely cold temperatures after a long period of natural and artificial selection. Selection and local adaptation are shaping populations. However, identifying loci associated with cold adaptation has been a major challenge. We used high-density SNP arrays and resequencing data to comprehensively analyze and compare the genomic selection signatures of Chinese northern and southern cattle, and elucidated several adaptive genes and alleles involved in cold adaptation. The complexity of genetic adaptation mechanism among different low-temperature adapted cattle breeds was also emphasized.

Coordinated alternation of DNA methylation and alternative splicing of PBRM1 affect bovine sperm structure and motility.

DNA methylation and gene alternative splicing drive spermatogenesis. In screening DNA methylation markers and transcripts related to sperm motility, semen from three pairs of full-sibling Holstein bulls with high and low motility was subjected to reduced representation bisulphite sequencing. A total of 948 DMRs were found in 874 genes (gDMRs). Approximately 89% of gDMR-related genes harboured alternative splicing events, including SMAD2, KIF17, and PBRM1. One DMR in exon 29 of PBRM1 with the highest 5mC ratio was found, and hypermethylation in this region was related to bull sperm motility. Furthermore, alternative splicing events at exon 29 of PBRM1 were found in bull testis, including PBRM1-complete, PBRM1-SV1 (exon 28 deletion), and PBRM1-SV2 (exons 28-29 deletion). PBRM1-SV2 exhibited significantly higher expression in adult bull testes than in newborn bull testes. In addition, PBRM1 was localized to the redundant nuclear membrane of bull sperm, which might be related to sperm motility caused by sperm tail breakage. Therefore, the hypermethylation of exon 29 may be associated with the production of PBRM1-SV2 in spermatogenesis. These findings indicated that DNA methylation alteration at specific loci could regulate gene splicing and expression and synergistically alter sperm structure and motility.